When working on complex molecular systems, managing what is visible and what is hidden can make or break the modeling experience. If you’re navigating crowded scenes or focusing on specific molecular properties, you’ve likely asked: How do I quickly control what I see without accidentally removing essential data?
In SAMSON, the integrative molecular design platform, visibility is more than just an on/off switch. If you’re using the Node Specification Language (NSL), understanding how visibility is managed within the propertyModel attribute space (short name: pm) can help streamline your workflow and eliminate visual clutter.
Three Layers of Visibility You Should Know
The visibility of property models in SAMSON is determined by three distinct but related attributes:
visible(pm.v): A high-level flag that determines if a node should be rendered or not.visibilityFlag(pm.vf): A more granular control used internally to reflect specific user or system-defined visibility settings.hidden(pm.h): Indicates negative visibility; if set totrue, the property model is hidden regardless of other flags.
When combined, these attributes give you precise control over what appears in your molecular scene.
Typical Use Case: Focused Analysis
Let’s suppose you’re analyzing a protein-ligand interaction but want to temporarily hide all additional property models (e.g., electrostatics, hydrophobic surfaces) to reduce clutter or focus on a specific region.
You can create a concise NSL query to find and control these nodes:
|
1 |
pm.v // Returns all visible property model nodes<br>not pm.v // Returns all hidden property model nodes |
Or, for detailed scenarios involving system-assigned visibility, you can use:
|
1 |
pm.vf false // Finds nodes that are not flagged as visible |
This level of control is especially helpful when working with scripting or building workflows that involve multiple steps where visibility needs to change dynamically.
Understanding Conflicts Between Flags
One common point of confusion: setting one flag (e.g., pm.v) to true doesn’t always guarantee the node will display if pm.h is true (i.e., the node is explicitly hidden). Knowing how these flags interplay can save time.
Useful tip: In most cases, use pm.v for global toggling, and inspect pm.h and pm.vf when you experience unexpected visibility behavior.
Quick Reference Table
| Attribute | Short Name | Values | Example |
|---|---|---|---|
visible |
v |
true, false |
pm.v |
visibilityFlag |
vf |
true, false |
pm.vf false |
hidden |
h |
true, false |
pm.h |
Once you get used to these visibility attributes, you’ll find yourself navigating large molecular models faster and with more confidence.
Learn more in the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.